The hero is a young boy who was frozen in a cryogenic sleep. With the aid of four sages, he learns that the world is about to be doomed again, and that he will need to find four elemental swords to fight Draygon's army and prevent him from making his goal of conquering the Tower a reality.

Crystalis contains examples of:

Ability Required to Proceed: All over the place, with the most frequent (and appearing the earliest) being walls that can only be destroyed if the hero has an appropriate orb to upgrade the Charged Attack of each sword.

After the End: The game is set after nuclear war destroyed most of humanity.

Every sword comes with a base level 1 charge. Most can charge to a level 2 attack after you acquire an orb to go with said sword (except the Crystalis sword, which also automatically comes with this), and the four elemental swords can hit a level 3 charge when an appropriate bracelet is equipped.

The Crystalis sword's apparent three charge levels is the result of a glitch and the sword was always meant to have just one charge level. If you go into your inventory (or the status screen) and come back out, the "extra" levels of charge disappear. Furthermore, assuming you have a bracelet equipped, if you avoid going into your inventory between receiving Crystalis and the battle with the tower's computer systems DYNA, you'll find that the "extra" levels do nothing.

Conspicuously Light Patch: Some sections of walls can be destroyed with the level 2 attack from particular swords, and they're all conspicuously visually different from the rest of the wall.

Excuse Plot: The GBC version of the game has this. The NES original had a surprisingly deep plot for an NES game back in the day, full of several plot twists that are likely able to catch the player off guard. The "plot" for the GBC version, however, can be summed up as: "There's a wizard. He's evil. Go kill him." It even goes as far as to spoil the major plot twist of the NES version in the very first opening cut scene of the game!

Four Is Death: On both sides really. There are four benevolent wisemen, but there are also four evil generals who work for Emperor Draygon.

Forced Level-Grinding: In the NES version, you cannot damage enemies or bosses if you aren't sufficiently leveled up. The GBC version averts this, which also makes it much harder.

Heroic Mime: Mostly played straight, as the hero has all of four lines, three of which are used to tell mortally wounded characters (first an Almost Dead Guy on Mt. Sabre, then Stom and Akahana in Shyron) to hold on if they want to maximize their remaining time before having a Critical Existence Failure.

Hero of Another Story: Kensu, up until the point he teaches you Flight. Where the other wisemen dedicate themselves to helping the hero, Kensu takes on the Empire himself. If not for a lucky shot from Karmine, he might have freed the other wisemen himself after Shyron fell.

Human Popsicle: The start of the game has the hero wake up from cryogenic sleep inside of a hidden cave. Later in the game, Mesia wakes up from a similar situation.

Humans Are Ugly: The elder of Oak doesn't like the smell of humans. In the GBC remake, it's one of the residents blocks the elder's house claiming he doesn't like that smell. That resident doesn't like the smell even after he accepts that humans are actually nice.

Improbable Power Discrepancy: Averted. DYNA is a pushover, and its only defense is a set of gatling guns. You easily defeat it with Crystalis, which the game manual notes is the most powerful weapon ever created.

King in the Mountain: Along with Mesia, your character is asleep until the time comes to either save the world or destroy it.

Lady Land: Amazones. They insist that men are forbidden in town. To purchase goods or rest at the inn, you must morph into a female form to trick them into letting you in.

La Résistance: The hero, Mesia, Zebu, Tornel, Athena, Kensou and Stom. Azteca also counts, since Draygon doesn't subvert it due to being rather separate from his 'creator' and also being an Enemy Within.

Mana Meter: It's a numerical gauge that the hero must draw from to cast spells or shoot level 3 sword attacks.

Mana Potion: Fruit of Power restores part of your magic. Magic Rings restore all of it.

Magical Mystery Doors: The floating tower has them in the GBC port. While each floor and door does look different, the correct path is marked by broken pillars with exposed wires. The final floor is a set of three doors with no indication which one is correct.

Magic Versus Science: The skills in the game include an array of common psychic tropes but are referred to in-game as spells, seemingly an inability to decide which they are if either. This could mean that these abilities are thought of as both or it could be a Shout-Out to Psycho Soldier due to the cameos made by Athena and Kensou.

Mind Screw: "Wait, were Azteca and Draygon the same person or were their minds linked somehow? And how does that work if Azteca was really an android the whole time? And why was he an android anyway?! I'm so confused!"

No Ontological Inertia: The GBA port has General Kelbesque cast a spell on Zebu that disintegrates him into a million pieces. Defeating the general causes Zebu to be restored and appear in the next room.

Smart Bomb: The final charged level of the Sword of Thunder just has a lightning bolt hit all enemies on-screen.

Sound of No Damage: There's a "clink" sound when hitting an enemy that's too far above you in level or that's immune to the sword you're currently wielding. Once you reach a high enough level, weaker enemies will "clink" when hitting you!

The Smurfette Principle: Of all the villains, the only woman working for Draygonia is Sabera. This stands out in particular because the heroic side has several women actively helping out.

Spam Attack: Equipping the Warrior's Ring would allow you to fire the level 1 attack of your currently equipped sword without charging.

Spread Shot: One of the two main advantages of the Sword of Thunder's charge attacks (the other being more sheer power as long as the enemy wasn't specifically immune to it). The first power fires three projectiles, while the version gained from the Ball of Thunder fires seven.

Speaks Fluent Animal: One of the side effects of the "Telepathy" spell is that it allows you to communicate with animals.

Sword Beam: All swords have a charge attack to launch a projectile. They become varied at higher charge levels where some of them are actually area attacks rather than crescents or line attacks.

Sword of Plot Advancement: The eponymous Crystalis is acquired just before the final battle and necessary to overcome the final obstacles in the game. It's a fusion of the Swords of Wind, Fire, Water, and Thunder which you collect throughout the game.

Tomato Surprise: In the Tower it is revealed that the Hero was one of the scientists who built the thing in the first place. Your job after awakening was to judge whether the remnants of humanity were worth saving and if the answer was no, to use the Tower to wipe them out. Being the Hero, you destroy the Tower instead.

Two Aliases, One Character: Portoa's Queen and the Fortune Teller both appear, but not at the same time and keep referring you to the other alias. Eventually, the dialog will start looping, requiring the hero to double back and use the newly acquired paralysis skill.

Villain: Exit, Stage Left: Generals Kelbesque, Sabera and Mado of Draygon's "Finest Four". Unlike the other boss enemies they flee upon being defeated the first time except for Karmine, who's only fought in Goa Fortress where you get to take all four down for good.

Welcome to Corneria: Using Telepathy in the GBC version always gives the same message all the time. This was not the case in the NES version, where the advice changes as you progress through the game, and where one of the contacts could remotely restore your MP.

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